Collagen-induced arthritis (CIA) and pristane-induced arthritis (PIA) in rats are well-established experimental animal models that have been used to gain insight into the pathogenesis of rheumatoid arthritis (RA), a chronic and commonly disabling disease with a prevalence of 1% in most populations. CIA, PIA and RA are complex trait diseases regulated by MHC and non-MHC genes. Non-MHC genes account for 50-75% of the genetic contribution to RA, yet, little is known about those genes. The underlying hypotheses of this proposal are that the non-MHC loci governing susceptibility to and severity of CIA and PIA in rats will be highly relevant to understanding the pathogenesis of RA and could generate new targets for the development of more specific therapies, as well new tools for diagnosis and prognosis. In experiments leading up to the present proposal, a genome-wide screen done in a F2 intercross between the MHC discordant inbred arthritis-susceptible DA and the arthritis-resistant F344 rat strains identified three non-MHC quantitative trait loci (QTL) Cia3, Cia5 and Cia6 on chromosomes 4, 10 and 8, respectively. The arthritis-regulatory effect of these QTLs was confirmed in genotype-guided congenic strains where the F344-derived interval was introgressed into the DA background. These QTL-congenic strains were protected and developed a significantly milder form of arthritis. Based on these prior studies, it is hypothesized that the robust and highly penetrant phenotype of CIA and PIA depends on the presence of susceptibility alleles at Cia3, Cia5 and Cia6. Additionally, Cia3 and Cia5 are located in regions homologous to those containing RA susceptibility genes, suggesting that the same genes might regulate arthritis on both species. This proposal aims at identifying and characterizing those genes. On aim 1 the construction of subcongenic strains will be completed in order to reduce the critical regions containing the arthritis genes to <1Mb. Subphenotypes relevant to arthritis will be identified and studied in congenics to obtain early clues to gene function and identity. On aim 2 candidate genes within the critical regions will be sequenced and analyzed for disease-causing polymorphisms/mutations that differentiate DA from F344. The identified genes and disease variants will be functionally characterized in in vitro and in vivo studies.